Bio/TreeIO/cluster.pm

   1 # $Id$
   2 #
   3 # BioPerl module for Bio::TreeIO::cluster
   4 #
   5 # Contributed by Guillaume Rousse <Guillaume-dot-Rousse-at-inria-dot-fr>
   6 #
   7 # Copyright INRIA
   8 #
   9 # You may distribute this module under the same terms as perl itself
  10
  11 # POD documentation - main docs before the code
  12
  13 =head1 NAME
  14
  15 Bio::TreeIO::cluster - A TreeIO driver module for parsing Algorithm::Cluster::treecluster() output
  16
  17 =head1 SYNOPSIS
  18
  19   # do not use this module directly
  20   use Bio::TreeIO;
  21   use Algorithm::Cluster;
  22   my ($result, $linkdist) = Algorithm::Cluster::treecluster(
  23     distances => $matrix
  24   );
  25   my $treeio = Bio::TreeIO->new(
  26     -format   => 'cluster',
  27     -result   =>  $result,
  28     -linkdist =>  $linkdist,
  29     -labels   =>  $labels
  30   );
  31   my $tree = $treeio->next_tree;
  32
  33 =head1 DESCRIPTION
  34
  35 This is a driver module for parsing Algorithm::Cluster::treecluster() output.
  36
  37 =head1 FEEDBACK
  38
  39 =head2 Mailing Lists
  40
  41 User feedback is an integral part of the evolution of this and other
  42 Bioperl modules. Send your comments and suggestions preferably to
  43 the Bioperl mailing list.  Your participation is much appreciated.
  44
  45   bioperl-l@bioperl.org                  - General discussion
  46   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  47
  48 =head2 Reporting Bugs
  49
  50 Report bugs to the Bioperl bug tracking system to help us keep track
  51 of the bugs and their resolution. Bug reports can be submitted via
  52 the web:
  53
  54   http://bugzilla.open-bio.org/
  55
  56 =head1 AUTHOR - Guillaume Rousse
  57
  58 Email Guillaume-dot-Rousse-at-inria-dot-fr
  59
  60 =head1 CONTRIBUTORS
  61
  62 Jason Stajich - jason-at-bioperl-dot-org
  63
  64 =head1 APPENDIX
  65
  66 The rest of the documentation details each of the object methods.
  67 Internal methods are usually preceded with a _
  68
  69 =cut
  70
  71
  72 # Let the code begin...
  73
  74
  75 package Bio::TreeIO::cluster;
  76 use strict;
  77
  78 use Bio::Event::EventGeneratorI;
  79 use IO::String;
  80
  81 use base qw(Bio::TreeIO);
  82
  83 =head2 new
  84
  85  Title   : new
  86  Usage   : my $obj = Bio::TreeIO::cluster->new();
  87  Function: Builds a new Bio::TreeIO::cluster object for reading Algorithm::Cluster::treecluster output
  88  Returns : Bio::TreeIO::cluster
  89  Args    :-result   => Algorithm::Cluster result
  90           -linkdist => distance between links
  91           -labels   => node labels
  92
  93 =cut
  94
  95 sub _initialize {
  96   my $self = shift;
  97   ($self->{_result},$self->{_linkdist},
  98    $self->{_labels}) = $self->_rearrange([qw
  99                                           (RESULT LINKDIST LABELS)],
 100                                          @_);
 101   $self->SUPER::_initialize(@_);
 102 }
 103
 104 =head2 next_tree
 105
 106  Title   : next_tree
 107  Usage   : my $tree = $treeio->next_tree
 108  Function: Gets the next tree in the stream
 109  Returns : Bio::Tree::TreeI
 110  Args    : none
 111
 112
 113 =cut
 114
 115 sub next_tree {
 116     my ($self) = @_;
 117     if( ! $self->{_result} ){
 118         $self->warn("Must provide value 'result' and 'linkdist' and 'labels' when initializing a TreeIO::cluster object");
 119         return;
 120     }
 121     $self->_eventHandler->start_document();
 122
 123     # build tree from the root
 124     $self->_eventHandler->start_element({Name => 'tree'});
 125     $self->_recurse(-1, 0);
 126     $self->_recurse(-1, 1);
 127     $self->_eventHandler->end_element({Name => 'tree'});
 128
 129     return $self->_eventHandler->end_document;
 130 }
 131
 132 sub _recurse {
 133     my ($self, $line, $column) = @_;
 134
 135     my $id  = $self->{_result}->[$line]->[$column];
 136     if ($id >= 0) {
 137         # leaf
 138         $self->debug("leaf $id\n");
 139         $self->debug("distance $self->{_linkdist}->[$line]\n");
 140         $self->debug("label $self->{_labels}->[$id]\n");
 141         $self->_eventHandler->start_element({Name => 'node'});
 142         $self->_eventHandler->start_element({Name => 'branch_length'});
 143         $self->_eventHandler->characters($self->{_linkdist}->[$line]);
 144         $self->_eventHandler->end_element({Name => 'branch_length'});
 145         $self->_eventHandler->start_element({Name => 'id'});
 146         $self->_eventHandler->characters($self->{_labels}->[$id]);
 147         $self->_eventHandler->end_element({Name => 'id'});
 148         $self->_eventHandler->start_element({Name => 'leaf'});
 149         $self->_eventHandler->characters(1);
 150         $self->_eventHandler->end_element({Name => 'leaf'});
 151         $self->_eventHandler->end_element({Name => 'node'});
 152     } else {
 153         # internal node
 154         $self->debug("internal node $id\n");
 155         $self->debug("distance $self->{_linkdist}->[$line]\n");
 156         $self->_eventHandler->start_element({Name => 'node'});
 157         $self->_eventHandler->start_element({Name => 'branch_length'});
 158         $self->_eventHandler->characters($self->{_linkdist}->[$line]);
 159         $self->_eventHandler->end_element({Name => 'branch_length'});
 160         $self->_eventHandler->start_element({Name => 'leaf'});
 161         $self->_eventHandler->characters(0);
 162         $self->_eventHandler->end_element({Name => 'leaf'});
 163         $self->_eventHandler->start_element({Name => 'tree'});
 164         my $child_id = - ($id + 1);
 165         $self->_recurse($child_id, 0);
 166         $self->_recurse($child_id, 1);
 167         $self->_eventHandler->end_element({Name => 'tree'});
 168         $self->_eventHandler->end_element({Name => 'node'});
 169
 170     }
 171 }
 172
 173 =head2 write_tree
 174
 175  Title   : write_tree
 176  Usage   :
 177  Function: Sorry not possible with this format
 178  Returns : none
 179  Args    : none
 180
 181
 182 =cut
 183
 184 sub write_tree{
 185     $_[0]->throw("Sorry the format 'cluster' can only be used as an input format");
 186 }
 187
 188 1;